The association between vaginal bacterial composition and miscarriage: a nested case-control study
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- United Kingdom
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Posterior fornix of vagina Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- spontaneous abortion Abortion, spontaneous,spontaneous abortion
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Viable control pregnancy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- First or second-trimester miscarriage
- Group 0 sample size Number of subjects in the control (unexposed) group
- 81
- Group 1 sample size Number of subjects in the case (exposed) group
- 77
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Chi-Square
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, gestational age
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 2A
Description:
Abundance in Group 1: decreased abundance in First or second-trimester miscarriage
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus sp. |
Revision editor(s): Titas
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- First trimester miscarriage
- Group 1 sample size Number of subjects in the case (exposed) group
- 64
- Sequencing type
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Not specified
- Statistical test
- Not specified
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: 2D
Description:
Abundance in Group 1: decreased abundance in First trimester miscarriage
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus sp. |
Revision editor(s): Titas
Signature 2
Source: Figure 2D + interpretation
Description: Samples deplete of Lactobacillus spp. display increased richness and diversity and colonization by potential pathogens.
Abundance in Group 1: increased abundance in First trimester miscarriage
NCBI | Quality Control | Links |
---|---|---|
Prevotella sp. | ||
Streptococcus | ||
Peptoniphilus | ||
Ureaplasma | ||
Dialister |
Revision editor(s): Titas
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- missed miscarriage
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- complete/incomplete miscarriage
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A missed miscarriage is when a baby has died in the womb, but the mother hasn't had any symptoms, such as bleeding or pain.
A complete miscarriage has taken place when all the pregnancy tissue has left your uterus.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Signature 1
Source: Figure 3
Description: Vaginal microbiota composition on the basis of incomplete and/or complete miscarriages
Abundance in Group 1: decreased abundance in complete/incomplete miscarriage
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus sp. |